Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Conservation of Protein Domains Over Different Proteins

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...

Directing Proteins to the Rough Endoplasmic Reticulum

Directing Proteins to the Rough Endoplasmic Reticulum

The organelle-specific signaling sequences direct proteins synthesized in the cytosol to their final destination like ER, mitochondria, peroxisomes, etc. Some of the proteins directed to ER are then trafficked via vesicles to other organelles within the cell or the extracellular environment through the Golgi complex. For example, the rough ER synthesizes soluble proteins for transportation to the lysosomes or secretion out of the cell. It can also synthesize transmembrane proteins that can...

Protein-Protein Interfaces

Protein-Protein Interfaces

Protein-protein Interfaces

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...

Protein Complex Assembly

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types. Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...

Protein Complex Assembly

Protein Complex Assembly

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Author Correction: Biophysical prediction of protein-peptide interactions and signaling networks using machine learning.

Nature methods·2026

Same author

AlphaFold as a prior: experimental structure determination conditioned on a pretrained neural network.

Nature methods·2026

Same author

Safety and immunogenicity of DNA omicron booster Alveavax-v1.2 in Ad26.COV2.S-vaccinated adults.

iScience·2025

Same author

Cryosectioning-enhanced super-resolution microscopy for single-protein imaging across cells and tissues.

Proceedings of the National Academy of Sciences of the United States of America·2025

Same author

hafoe: an interactive tool for the analysis of chimeric AAV libraries after random mutagenesis.

Gene therapy·2025

Same author

DNA-PAINT Imaging with Hydrogel Imprinting and Clearing.

ACS sensors·2025

Same journal

ClairS: a deep-learning method for long-read tumor-normal pair somatic small variant calling.

Nature methods·2026

Same journal

RNAbpFlow: base pair-augmented SE(3) flow matching for conditional RNA 3D structure generation.

Nature methods·2026

Same journal

Spatio-DARLIN enables robust and efficient in situ lineage tracing in mice at single-cell resolution.

Nature methods·2026

Same journal

EasyGrid: a versatile platform for automated cryo-EM sample preparation and quality control.

Nature methods·2026

Same journal

Cloud-based microscope enables live neuroimaging for 24 h and beyond with worldwide access.

Nature methods·2026

Same journal

Deep molecular profiling in three dimensions.

Nature methods·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jan 5, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Unified rational protein engineering with sequence-based deep representation learning.

Ethan C Alley^1,2, Grigory Khimulya, Surojit Biswas^1,3

¹Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.

|October 23, 2019

Summary

This summary is machine-generated.

Deep learning models, like UniRep, can understand protein features from amino acid sequences. This approach enhances protein engineering efficiency and function prediction.

More Related Videos

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Author Spotlight: Advancing Alzheimer's Research – Exploring Early Detection and Multi-Omics Approaches

Author Spotlight: Advancing Alzheimer's Research – Exploring Early Detection and Multi-Omics Approaches

Published on: December 15, 2023

Related Experiment Videos

Last Updated: Jan 5, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Author Spotlight: Advancing Alzheimer's Research – Exploring Early Detection and Multi-Omics Approaches

Author Spotlight: Advancing Alzheimer's Research – Exploring Early Detection and Multi-Omics Approaches

Published on: December 15, 2023

Area of Science:

Computational biology
Protein engineering
Machine learning

Background:

Rational protein design necessitates a comprehensive understanding of protein function.
Current methods often lack a unified representation of diverse protein features.

Purpose of the Study:

To develop a deep learning approach for distilling fundamental protein features from unlabeled amino acid sequences.
To create a unified, semantically rich representation grounded in structural, evolutionary, and biophysical properties.

Main Methods:

Application of deep learning to unlabeled amino acid sequences.
Development of a unified representation (UniRep) capturing fundamental protein features.
Building simple models on top of the UniRep representation.

Main Results:

UniRep models generalize to unseen sequence spaces.
Accurate prediction of protein stability for natural and designed proteins.
Quantitative function prediction for diverse mutants, competitive with state-of-the-art methods.
Achieved two orders of magnitude efficiency improvement in protein engineering tasks.

Conclusions:

UniRep provides a versatile summary of fundamental protein features.
The data-driven approach is broadly applicable across protein engineering informatics.
Enables more efficient and accurate protein design and analysis.